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Language Skills

R
Python
Git/GitHub
Bash
docker

Disclaimer

The long-form version of my CV is available as a pdf

Made with the R package datadrivencv and pagedown.

The source code is available at github.com/dzhang32/cv.

Last updated on 2021-12-21.

Main

David Zhang

Experienced bioinformatician who enjoys learning and applying the best practices for method development. I focus on developing robust, user-friendly tools that harness transcriptomic data to improve the rate of genetic diagnosis.

Education

PhD, Bioinformatics

University College London

London, UK

Present - 2017

  • Thesis: Using transcriptomics to improve the genetic diagnosis rate of rare disease patients.

MSc, Neuroscience

University College London

London, UK

2016 - 2015

  • Thesis: The role of mitochondrial dysfunction in Xerodoma pigmentosum
  • Grade: Merit (68%)
  • Awarded post-graduate support scheme bursary (£10,000)

BSc, Biomedical science

University College London

London, UK

2015 - 2012

  • Thesis: Investigating the function of CYFIP1 in the development of rat hippocampal neurons.
  • Grade: 2:1 (69%)

H.S.

Queen Elizabeth’s School

Barnet, UK

2012 - 2007

  • Grades: Maths (A*), Biology (A*), Chemistry (A*), Sociology (A).

Work Experience

Bioinformatician internship (2 months)

Verge Genomics

Remote, US

2021

  • Goal: Set up an aberrant splicing detection pipeline for drug target discovery in C9orf72 ALS patients.
  • Used docker to setup a reproducible workflow for running aberrant splicing analyses on an AWS instance.

Software & programming

Bioconductor packages

N/A

N/A

Present - 2020

  • dasper: Detection of aberrant splicing events in RNA-sequencing. Author and maintainer.
  • megadepth: BigWig and BAM related utilities. An R wrapper for the megadepth software developed by Chris Wilks. Co-author and maintainer.
  • ODER: Optimising the definition of Expressed Regions. Submitted to Bioconductor. Co-author and maintainer.

Python packages

N/A

N/A

Present - 2021

  • codino converts a codon design to the expected amino acid frequencies, and vice versa. Author and maintainer.

Web scraping

N/A

N/A

2021

  • Applied the python packages Beautiful Soup and Selenium to web scrape information on all UK biotechnology companies.

Data science blog

N/A

N/A

2021

  • Chess-related blog post was selected for the hand-on-tutorials column in Towards Data Science, which displays pieces that highlight best practices of data science.
  • Applied popular data science packages in python to analyse chess.com data.

Teaching Experience

Developing Bioconductor packages

University College London

Virtual Event

2020

  • Hosted workshop on best practices for developing Bionconductor packages using biocthis.

Unit testing using testthat edition 3

rstats club

Virtual Event

2020

  • Talk regarding unit testing fundamentals, the importance of testing and new features released in the R package testthat edition 3.

R fundamentals

Clinician Coders

London, UK

2020 - 2018

  • Developed materials and lead workshops that aimed to teach R fundamentals to clinicians.

Selected Publications

recount3: summaries and queries for large-scale RNA-seq expression and splicing

Genome Biology

N/A

2021

  • Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B
  • Role: Adviser.
  • DOI: https://doi.org/10.1186/s13059-021-02533-6

Developmental Consequences of Defective ATG7-Mediated Autophagy in Humans

The New England Journal of Medicine

N/A

2021

  • Collier J, Guissart C, Oláhová M, Sasorith S, Piron-Prunier F, Suom Fi, Zhang D, Martinez-Lopez N, Leboucq N, Bahr A, Azzarello-Burri S, Reich S, Schöls L, Polvikoski TM, Meyer P, Larrieu L, Schaefer AM, Alsaif HS, Alyamani S, Zuchner S, Barbosa IA, Deshpande C, Pyle A, Rauch A, Synofzik M, Alkuraya FS, Rivier F, Ryten M, McFarland R, Delahodde A, McWilliams TG, Koenig M, and Taylor RW.
  • Role: Analyst
  • DOI: https://doi.org/10.1056/NEJMoa1915722

Megadepth: efficient coverage quantification for BigWigs and BAMs

Bioinformatics

N/A

2021

Integration of eQTL and Parkinson’s disease GWAS data implicates 11 disease genes

Jama Neurology

N/A

2021

  • Kia DA, Zhang D, Guelfi S, Manzoni C, Hubbard L, United Kingdom Brain Expression Consortium (UKBEC), International Parkinson’s Disease Genomics Consortium (IPDGC), Reynolds RH, Botía JA, Ryten M, Ferrari R, Lewis PA, Williams N, Trabzuni D, Hardy J, Wood NW.
  • Role: Co-first author.
  • DOI: https://doi.org/10.1001/jamaneurol.2020.5257

Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders.

Science advances

N/A

2020

  • Zhang D, Guelfi S, Ruiz SG, Costa B, Reynolds RH, D’Sa K, Liu W, Courtin T, Peterson A, Jaffe AE, Hardy J, Botia JA, Collado-Torres L and Ryten M.
  • Role: First Author.
  • DOI: https://doi.org/10.1126/sciadv.aay8299